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<pre class="western" style="margin-bottom: 0.5cm;">yes, all angles and dihedrals are present but wath I mean is for example the sp2 <br>carbon of carbonate ion, I only need 2 angles to completely describe the <br>in-plane motion of the 3 oxygen atoms. Is correct to include all three in <br>plane coordinates?, What <span id="result_box" class="short_text"><span style="background-color: rgb(230, 236, 249); color: rgb(0, 0, 0);" title="">possible </span></span>differences in the result from the MD calculation <br>could be between one or the other situation?. <br><br>Thanks in advance!<span id="result_box" class="short_text"><span style="background-color: rgb(255, 255, 255); color: rgb(0, 0, 0);" title=""></span></span></pre>
<br><br>> Date: Wed, 16 Jun 2010 12:52:32 +0200<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] redundancies in the .itp file<br>> <br>> On 2010-06-16 00.50, Víctor Bahamonde wrote:<br>> > Dear users<br>> ><br>> ><br>> > I have created a .itp file with the program TopolGen, published in the<br>> > website of GROMACS. to review the angles, I see that there are<br>> > redundancies. This will affect the results of molecular dynamics<br>> > calculation?. What should I do with them? (delete?)<br>> Yes. You have to review any such topology carefully. Please check <br>> whether all angles and dihedrals (in particular impropers) are present <br>> as well.<br>> > Thanks in advance!<br>> ><br>> ><br>> > ------------------------------------------------------------------------<br>> > Ahora Hotmail es un 70% más veloz. Acceder a tu casilla nunca fue tan<br>> > rápido. Ver más <http://www.descubrehotmail.com/velocidad.asp ><br>> ><br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>> spoel@xray.bmc.uu.se http://folding.bmc.uu.se<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Acceder a tu casilla ahora es mucho más rápido. Ahora Hotmail es un 70% más veloz. <a href='http://www.descubrehotmail.com/velocidad.asp ' target='_new'>Conoce más</a></body>
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